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Error when compiling in Linux Ubuntu VM

Category: 
Compilation

Hi, good day everyone, 

I was trying to compile Rosetta 3 and after running smoothly for two hours it stopped, and I got the following error message: 

g++: internal compiler error: Killed (program cc1plus)

Please submit a full bug report,

with preprocessed source if appropriate.

See <file:///usr/share/doc/gcc-7/README.Bugs> for instructions.

scons: *** [build/src/release/linux/5.3/64/x86/gcc/7/default/core/io/pose_from_sfr/chirality_resolution.os] Error 4

Post Situation: 

How to add my own .cc and .hh file

Category: 
Compilation

Hello,i use scons to complie.

Recently,I write some class in .cc and .hh files , when i #include<~path/name.hh>,i find that it did not compile .cc files. I have read sconstruct file but do not know how to add my own file to compile with.

Please give me some help

Post Situation: 

Relaxation vs minimisation

Category: 
Structure prediction
Scoring
PyRosetta

Hi all,

I am very new to the computational structural biology community and I have tried to model a structure by using a software which runs MODELLER on the background. However, my result shows a number of steric clashes and a very high fa_rep when I calculate it with PyRosetta. I am therefore trying to improve the structure before moving on with the rest of my analysis. 

Post Situation: 

antibody_numbering_converter cannot recognize the IMGT scheme

Category: 
Docking

To whom it may concern:

Hi I want to convert my antibody structure from Chothia to IMGT. I use the following command and get an error "ERROR: Illegal value specified for option -antibody:output_ab_scheme : IMGT". I am wondering is the IMGT scheme already cancelled in the number converter program? This is a 2019.35.60890 version.

/home/rosetta_bin_linux_2019.35.60890_bundle/main/source/bin/antibody_numbering_converter.linuxgccrelease -input_ab_scheme Chothia -output_ab_scheme IMGT -s 1ahw_chothia.pdb

 

Best regards,

Post Situation: 

MotifGraft error: "Residue connection id changed when creating a new residue at seqpos"

Category: 
Design

Hello everyone,

I am trying to use MotifGraft mover to graft an epitope to a scaffold protein (actually there is a structure library, parsed with -l list).

The xml script is attached.

My command line is as follow (I am first trying a very loose boundary conditions, I'm aware about the higher RMSD/atom_clash values):

Post Situation: 

Distorted metal coordination geometry after relaxation (SetupMetalMover was used, fold tree and constraints were set manually)

Category: 
Design
Scoring
Constraints
PyRosetta

 

Hello,

I am trying to relax Zn containing peptides like zinc fingers, but always got distorted geometries of the coordination site and much higher scores after the relax. Still, the rest of the peptide looks nice.

Post Situation: 

Centroid mode minimization

Category: 
Structure prediction

Hi everyone,

I was wondering if there is something like the Relax Application but to use it directly in centroid mode. I know AbInitio uses fragment insertion to start building structures in centroid mode that are later fed to the All-Atom relax application, but is there something that can do a montecarlo local exploration without leaving centroid representation?

Post Situation: 

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